Bioconductor Single Package Builder - Build History

Snapshot Date:

URL: https://git.bioconductor.org/packages/MultiRNAflow

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
nebbiolo1	Linux (Ubuntu 22.04.1 LTS)/x86_64	OK	TIMEOUT	skipped	OK

nebbiolo1 Summary

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Package: MultiRNAflow

Version: 0.99.1

RVersion: 4.3

BiocVersion: 3.17

BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data MultiRNAflow

BuildTime: 4 minutes 25.93 seconds

CheckCommand: BiocCheckGitClone('MultiRNAflow') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2934/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2934/bd41fd9a4a9f5755b0ea074dc799d9253663d93b/MultiRNAflow.install-out.txt MultiRNAflow_0.99.1.tar.gz && BiocCheck('MultiRNAflow_0.99.1.tar.gz', `new-package`=TRUE)

CheckTime: 5 minutes 24.15 seconds

BuildBinCommand:

BuildBinTime:

PackageFileSize: 3798.97 KiB

BuildID:: MultiRNAflow_20230331230452

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: MultiRNAflow. Starting Build package. Starting Check package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: -9.

nebbiolo1 BUILD SRC output

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===============================

 R CMD BUILD

===============================

* checking for file ‘MultiRNAflow/DESCRIPTION’ ... OK
* preparing ‘MultiRNAflow’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘MultiRNAflow_0.99.1.tar.gz’

nebbiolo1 CHECK output

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===============================

 BiocCheckGitClone('MultiRNAflow')

===============================

─ BiocCheckVersion: 1.35.17
─ BiocVersion: 3.17
─ Package: MultiRNAflow
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2934/bd41fd9a4a9f5755b0ea074dc799d9253663d93b/MultiRNAflow
─ platform: unix
─ isTarBall: FALSE

* Checking valid files...
    * ERROR: System files found that should not be Git tracked.
      MultiRNAflow.Rproj
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

─ BiocCheck results ──
1 ERRORS | 0 WARNINGS | 0 NOTES

For more details, run
    browseVignettes(package = 'BiocCheck')




===============================

 R CMD CHECK

===============================

* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2934/bd41fd9a4a9f5755b0ea074dc799d9253663d93b/MultiRNAflow.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MultiRNAflow/DESCRIPTION’ ... OK
* this is package ‘MultiRNAflow’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MultiRNAflow’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [41s/41s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'DATAplotExpressionGenes':
DATAplotExpressionGenes
  Code: function(ExprData, Vector.row.gene, Column.gene,
                 Group.position, Time.position, Individual.position,
                 Color.Group = NULL, Plot.Expression = TRUE,
                 path.result = NULL, Name.folder.profile = NULL)
  Docs: function(ExprData, Vector.row.gene, Column.gene,
                 Group.position, Time.position, Individual.position,
                 Color.Group = NULL, path.result = NULL,
                 Name.folder.profile = NULL)
  Argument names in code not in docs:
    Plot.Expression
  Mismatches in argument names:
    Position: 8 Code: Plot.Expression Docs: path.result
    Position: 9 Code: path.result Docs: Name.folder.profile

Codoc mismatches from documentation object 'DEanalysisGlobal':
DEanalysisGlobal
  Code: function(RawCounts, Column.gene, Group.position, Time.position,
                 Individual.position, pval.min = 0.05, pval.vect.t =
                 NULL, log.FC.min = 1, LRT.supp.info = FALSE,
                 Plot.DE.graph = TRUE, path.result = NULL,
                 Name.folder.DE = NULL)
  Docs: function(RawCounts, Column.gene, Group.position, Time.position,
                 Individual.position, pval.min = 0.05, pval.vect.t =
                 NULL, log.FC.min = 1, LRT.supp.info = FALSE,
                 path.result = NULL, Name.folder.DE = NULL)
  Argument names in code not in docs:
    Plot.DE.graph
  Mismatches in argument names:
    Position: 10 Code: Plot.DE.graph Docs: path.result
    Position: 11 Code: path.result Docs: Name.folder.DE

Codoc mismatches from documentation object 'DEanalysisGroup':
DEanalysisGroup
  Code: function(DESeq.result, pval.min = 0.05, log.FC.min = 1,
                 LRT.supp.info = TRUE, Plot.DE.graph = TRUE,
                 path.result = NULL, SubFile.name = NULL)
  Docs: function(DESeq.result, pval.min = 0.05, log.FC.min = 1,
                 LRT.supp.info = TRUE, path.result = NULL, SubFile.name
                 = NULL)
  Argument names in code not in docs:
    Plot.DE.graph
  Mismatches in argument names:
    Position: 5 Code: Plot.DE.graph Docs: path.result
    Position: 6 Code: path.result Docs: SubFile.name

Codoc mismatches from documentation object 'DEanalysisTime':
DEanalysisTime
  Code: function(DESeq.result, pval.min = 0.05, pval.vect.t = rep(0.05,
                 times = 6), log.FC.min = 1, LRT.supp.info = FALSE,
                 Plot.DE.graph = TRUE, path.result = NULL, SubFile.name
                 = NULL)
  Docs: function(DESeq.result, pval.min = 0.05, pval.vect.t = rep(0.05,
                 times = 6), log.FC.min = 1, LRT.supp.info = FALSE,
                 path.result = NULL, SubFile.name = NULL)
  Argument names in code not in docs:
    Plot.DE.graph
  Mismatches in argument names:
    Position: 6 Code: Plot.DE.graph Docs: path.result
    Position: 7 Code: path.result Docs: SubFile.name

Codoc mismatches from documentation object 'DEanalysisTimeAndGroup':
DEanalysisTimeAndGroup
  Code: function(DESeq.result, LRT.supp.info = TRUE, log.FC.min,
                 pval.min, pval.vect.t, Plot.DE.graph = TRUE,
                 path.result, SubFile.name)
  Docs: function(DESeq.result, LRT.supp.info = TRUE, log.FC.min,
                 pval.min, pval.vect.t, path.result, SubFile.name)
  Argument names in code not in docs:
    Plot.DE.graph
  Mismatches in argument names:
    Position: 6 Code: Plot.DE.graph Docs: path.result
    Position: 7 Code: path.result Docs: SubFile.name

Codoc mismatches from documentation object 'DEplotHeatmaps':
DEplotHeatmaps
  Code: function(Res.DE.analysis, ColumnsCriteria = 2, Set.Operation =
                 "union", NbGene.analysis = 20, Color.Group = NULL,
                 SizeLabelRows = 5, SizeLabelCols = 5, Display.plots =
                 TRUE, Save.plots = FALSE)
  Docs: function(Res.DE.analysis, ColumnsCriteria = 2, Set.Operation =
                 "union", NbGene.analysis = 20, Color.Group = NULL,
                 SizeLabelRows = 5, SizeLabelCols = 5, Save.plots =
                 FALSE)
  Argument names in code not in docs:
    Display.plots
  Mismatches in argument names:
    Position: 8 Code: Display.plots Docs: Save.plots

Codoc mismatches from documentation object 'DEplotVolcanoMA':
DEplotVolcanoMA
  Code: function(Res.DE.analysis, NbGene.plotted = 2, SizeLabel = 3,
                 Display.plots = TRUE, Save.plots = FALSE)
  Docs: function(Res.DE.analysis, NbGene.plotted = 2, SizeLabel = 3,
                 Save.plots = FALSE)
  Argument names in code not in docs:
    Display.plots
  Mismatches in argument names:
    Position: 4 Code: Display.plots Docs: Save.plots

Codoc mismatches from documentation object 'GSEAQuickAnalysis':
GSEAQuickAnalysis
  Code: function(Res.DE.analysis, ColumnsCriteria = 1,
                 ColumnsLog2ordered = NULL, Set.Operation = "union",
                 Organism = "hsapiens", MaxNumberGO = 20, Background =
                 FALSE, Display.plots = TRUE, Save.plots = FALSE)
  Docs: function(Res.DE.analysis, ColumnsCriteria = 1,
                 ColumnsLog2ordered = NULL, Set.Operation = "union",
                 Organism = "hsapiens", MaxNumberGO = 20, Background =
                 FALSE, Save.plots = FALSE)
  Argument names in code not in docs:
    Display.plots
  Mismatches in argument names:
    Position: 8 Code: Display.plots Docs: Save.plots

Codoc mismatches from documentation object 'HCPCanalysis':
HCPCanalysis
  Code: function(ExprData, Column.gene, Group.position, Time.position,
                 Individual.position, sample.deletion, Supp.del.sample
                 = FALSE, gene.deletion, Plot.HCPC = TRUE, Color.Group
                 = NULL, Phi, Theta, Cex.point, epsilon, Cex.label,
                 D3.mouvement = FALSE, path.result = NULL,
                 Name.folder.hcpc = NULL)
  Docs: function(ExprData, Column.gene, Group.position, Time.position,
                 Individual.position, sample.deletion, Supp.del.sample
                 = FALSE, gene.deletion, Color.Group = NULL, Phi,
                 Theta, Cex.point, epsilon, Cex.label, D3.mouvement =
                 FALSE, path.result = NULL, Name.folder.hcpc = NULL)
  Argument names in code not in docs:
    Plot.HCPC
  Mismatches in argument names (first 3):
    Position: 9 Code: Plot.HCPC Docs: Color.Group
    Position: 10 Code: Color.Group Docs: Phi
    Position: 11 Code: Phi Docs: Theta

Codoc mismatches from documentation object 'MFUZZanalysis':
MFUZZanalysis
  Code: function(ExprData, Column.gene, Group.position, Time.position,
                 Individual.position, DataNumberCluster, Method =
                 "hcpc", Max.clust = 10, Membership, Min.std = 0.1,
                 Plot.Mfuzz = TRUE, path.result = NULL,
                 Name.folder.mfuzz = NULL)
  Docs: function(ExprData, Column.gene, Group.position, Time.position,
                 Individual.position, DataNumberCluster, Method =
                 "hcpc", Max.clust = 10, Membership, Min.std = 0.1,
                 path.result = NULL, Name.folder.mfuzz = NULL)
  Argument names in code not in docs:
    Plot.Mfuzz
  Mismatches in argument names:
    Position: 11 Code: Plot.Mfuzz Docs: path.result
    Position: 12 Code: path.result Docs: Name.folder.mfuzz

Codoc mismatches from documentation object 'MFUZZclustersNumber':
MFUZZclustersNumber
  Code: function(ExprData, Column.gene, Group.position, Time.position,
                 Individual.position, Method = "hcpc", Max.clust,
                 Min.std = 0.1, Plot.Cluster = TRUE, path.result =
                 NULL)
  Docs: function(ExprData, Column.gene, Group.position, Time.position,
                 Individual.position, Method = "hcpc", Max.clust,
                 Min.std = 0.1, path.result = NULL)
  Argument names in code not in docs:
    Plot.Cluster
  Mismatches in argument names:
    Position: 9 Code: Plot.Cluster Docs: path.result

Codoc mismatches from documentation object 'PCAanalysis':
PCAanalysis
  Code: function(ExprData, Column.gene, Group.position, Time.position,
                 Individual.position, gene.deletion, sample.deletion,
                 Supp.del.sample = FALSE, Plot.PCA = TRUE,
                 Mean.Accross.Time = FALSE, Color.Group = NULL, Phi,
                 Theta, Cex.point, Cex.label, epsilon, D3.mouvement =
                 FALSE, path.result = NULL, Name.folder.pca = NULL)
  Docs: function(ExprData, Column.gene, Group.position, Time.position,
                 Individual.position, Mean.Accross.Time, gene.deletion,
                 sample.deletion, Supp.del.sample = FALSE, Color.Group
                 = NULL, Phi, Theta, Cex.point, Cex.label, epsilon,
                 D3.mouvement = FALSE, path.result = NULL,
                 Name.folder.pca = NULL)
  Argument names in code not in docs:
    Plot.PCA
  Mismatches in argument names (first 3):
    Position: 6 Code: gene.deletion Docs: Mean.Accross.Time
    Position: 7 Code: sample.deletion Docs: gene.deletion
    Position: 8 Code: Supp.del.sample Docs: sample.deletion
  Mismatches in argument default values:
    Name: 'Mean.Accross.Time' Code: FALSE Docs: 

Codoc mismatches from documentation object 'PCAgraphics':
PCAgraphics
  Code: function(ExprData, Column.gene, Group.position, Time.position,
                 Individual.position, gene.deletion, sample.deletion,
                 Supp.del.sample = FALSE, Plot.PCA = TRUE,
                 Mean.Accross.Time = FALSE, Color.Group = NULL,
                 D3.mouvement = FALSE, Phi, Theta, Cex.point,
                 Cex.label, epsilon, path.result = NULL, Name.file.pca
                 = NULL)
  Docs: function(ExprData, Column.gene, Group.position, Time.position,
                 Individual.position, Mean.Accross.Time, gene.deletion,
                 sample.deletion, Supp.del.sample, Color.Group = NULL,
                 D3.mouvement = FALSE, Phi, Theta, Cex.point,
                 Cex.label, epsilon, path.result = NULL, Name.file.pca
                 = NULL)
  Argument names in code not in docs:
    Plot.PCA
  Mismatches in argument names (first 3):
    Position: 6 Code: gene.deletion Docs: Mean.Accross.Time
    Position: 7 Code: sample.deletion Docs: gene.deletion
    Position: 8 Code: Supp.del.sample Docs: sample.deletion
  Mismatches in argument default values:
    Name: 'Supp.del.sample' Code: FALSE Docs: 
    Name: 'Mean.Accross.Time' Code: FALSE Docs: 

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [93s/93s] OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
DEanalysisTimeAndGroup 8.966  0.568   9.535
DEplotVolcanoMA        7.800  0.464   8.264
DEplotHeatmaps         6.104  0.376   6.480
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [10s/10s]
 [10s/10s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [5s/4s] OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/pkgbuild/packagebuilder/workers/jobs/2934/bd41fd9a4a9f5755b0ea074dc799d9253663d93b/MultiRNAflow.Rcheck/00check.log’
for details.






===============================

 BiocCheck('MultiRNAflow_0.99.1.tar.gz')

===============================

─ BiocCheckVersion: 1.35.17
─ BiocVersion: 3.17
─ Package: MultiRNAflow
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/RtmpVFmVOm/file33f2971b49fe32/MultiRNAflow
─ installDir: /tmp/RtmpVFmVOm/file33f297127c417d
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2934/bd41fd9a4a9f5755b0ea074dc799d9253663d93b/MultiRNAflow.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
    * NOTE: Update R version dependency from 4.2 to 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
    * NOTE: Consider adding these automatically suggested biocViews:
      Microarray
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
    * NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
Warning in remind_sweave(if (in.file) input, sweave_lines) :
  It seems you are using the Sweave-specific syntax in line(s) 48, 7, 3432; you may need Sweave2knitr("/tmp/RtmpVFmVOm/file33f2971b49fe32/MultiRNAflow/vignettes//MultiRNAflow_vignette.Rnw") to convert it to knitr
 ERROR
TIMEOUT: BiocCheck exceeded 15mins

nebbiolo1 BUILD BIN output

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